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- PDB-2jyh: Rigid-body refinement of the tetraloop-receptor RNA complex -

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Basic information

Entry
Database: PDB / ID: 2jyh
TitleRigid-body refinement of the tetraloop-receptor RNA complex
ComponentsRNA (43-MER)
KeywordsRNA/RNA / RNA structure / RNA-RNA complex / tetraloop-receptor / GAAA-tetraloop / RNA global structure
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsThe deposited structures were calculated using a rigid-body refinement protocol and the SAXS data
AuthorsZuo, X. / Wang, J. / Foster, T.R. / Schwieters, C.D. / Tiede, D.M.
CitationJournal: To be Published
Title: Rigid-body refinement of the tetraloop-receptor RNA complex
Authors: Zuo, X. / Wang, J. / Foster, T.R. / Schwieters, C.D. / Tiede, D.M. / Butcher, S.E. / Wang, Y.
History
DepositionDec 13, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (43-MER)
B: RNA (43-MER)


Theoretical massNumber of molelcules
Total (without water)27,7472
Polymers27,7472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (43-MER)


Mass: 13873.258 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The deposited structures were calculated using a rigid-body refinement protocol and the SAXS data
NMR experimentType: 3D 1H-13C NOESY

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Sample preparation

DetailsContents: 8 mg/ml (w/v) Tetraloop-receptor RNA/RNA complex, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 8 w/v / Component: Tetraloop-receptor RNA:RNA complex
Sample conditionsIonic strength: 20 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHNot releasedSchwieters, C.D. et al.refinement
X-PLOR NIHNot releasedSchwieters, C.D. et al.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A modified SA using a rigid-body refinement protocol
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 5

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